We have developed a MAGE-ML export feature in collaboration with the European Bioinformatics Institute (EBI).

There is a two-photon intravital microscope available in the laboratory. It was used, among other things, to analyze the infiltration and destruction of solid tumors by CTLs.

This bioassay is a list of standardized procedures, which enables to use the dendritic cells as tools for the determination of the effects of new chemical compounds on dendritic cell capacity to produce type I IFNs. The selected molecules could be potential new vaccine adjuvants.

The FACS analyzer avaiable to the lab is used, among other things, to assess protein expression of tumor antigens or soluble proteins.

There is a Luminex flow cytometer available in the lab. It is used, among other things, for assaying of cytokines in B-CLL patients treated with Apo-DC +/- GM-CSF.

The MRI facility available in the laboratory is used, among other things, to image vaccines.

The gene gun system available to the laboratory was used, e.g., for micro-particle bombardment of murine skin.

The lab has a midi-MACS magnetic cell sorting device by Miltenyi Biotec, Bergisch-Gladbach, Germany, that is used, e.g., to isolate monocytes from PBMC.

The laboratory has expertise in the use of MACS anti-CD14 microbeads by Miltenyi Biotec, Bergisch-Gladbach, Germany. They were used for isolation of monocytes from PBMCs.

The Genopolis microarray database serves as an easy interface for the data generated by the Affymetrix GeneChip platform. DC transcriptomic data produced in the past 4 years has made been an accessible resource for data sharing and data integration accessible to all the DC community. The experiments on mice and rat are currently being annotated and conserved in the Genopolis database. Direct access to the primary data held in the Biopolo database is responsibility of the BIOPOLO Project Management System (see http://www.biopolo.it/).

Our laboratory has expertise in applying a fluorescence microscopy method to analyse proximal signalling events induced by cross-linking C-type lectins.

Experience has been gained in identifying DC presenting a specific peptide via a sensitive immunofluorescent staining technique.

Our laboratory has a mass spectrometer at its disposal.

Pathway Processor is a tool for integrating whole-genome expression results into metabolic networks.

This platform with its state-of-the-art mass spectrometry facilities is led by Mann (P33). To enhance the platform, two additional groups were recruited as Third Parties: P114 Edwin Lasonder in Nijmegen (NL), and P113 Juri Rappsilber in Edinburgh (GB). The mass spectrometer has been used, for instance, to identify and quantify chemokine dependent tyrosine phosphorylation events. Furthermore, the success of SILAC labelling was analysed using the mass spectrometer.

In the DC-THERA effort to create new dendritic cell-based therapies, a wide range of information arising from genomics, proteomics, molecular cell biology and pre-clinical models is gathered and applied to the conduction of clinical trials. The DC-THERA Directory is intended to collect and semantically organize this data and to serve as a tool for collaboration among researchers and as a reference point for the information contained. As such it is a directory that provides summarized information and relations between resources and people involved. In particular, we ...

RDFScape is a plugin that has been developed to extend a software oriented to biological analysis with support for reasoning on ontologies in the semantic web framework. We show with this plugin how the use of ontological knowledge in biological analysis can be extended through the use of inference. In particular, we present two examples relative to ontologies representing biological pathways: we demonstrate how these can be abstracted and visualized as interaction networks, and how reasoning on causal dependencies within elements of pathways can be implemented. A co...

Microarray and gene expression are fundamental tools of nowadays Biology research. While standard formats and software systems have been developed to represent and publicly share information about microarray experiments, existing computational solutions give limited support to the representation of the outcomes, experimental hypotheses or conclusions about biological questions that are dealt with in gene expression analysis. We propose an OWL-based model and a Semantic Web-based approach to address the issue. We show that the formalization of microarray-related knowle...

Our laboratory has an Amaxa electroporator at its disposal. The electroporator is used, among other things, for the transfection of immature DCs with different constructs encoding for the oncogene Her-2/neu and as control PSA.

This FACS analyser that is available to us is used, e.g., for the analysis of dendritic cells.